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Update sceasy to 0.0.7 #294

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Update sceasy to 0.0.7 #294

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fdb3fca
Update sceasy_macros.xml to 0.0.7
pcm32 Apr 29, 2023
508f602
Set to galaxy0
pcm32 Apr 29, 2023
199f45c
Adds test-data and tests
pcm32 Apr 29, 2023
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26 changes: 26 additions & 0 deletions tools/tertiary-analysis/sceasy/get_test_data.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
#!/usr/bin/env bash

mkdir -p test-data

BASENAME_FILE='E-MTAB-6077-3k_features_90_cells'

LOOM_LINK='https://drive.google.com/uc?export=download&id=1qNk5cg8hJG3Nv1ljTKmUEnxTOf11EEZX'
SCE_LINK='https://drive.google.com/uc?export=download&id=1UKdyf3M01uAt7oBg93JfmRvNVB_jlUKe'
H5AD_LINK='https://drive.google.com/uc?export=download&id=1YpE0H_t_dkh17P-WBhPijKvRiGP0BlBz'
RDS_LINK='https://drive.google.com/uc?export=download&id=1KW_GX6xznSUpWRWUykpNaSbAhyClf7_n'

function get_data {
local link=$1
local fname=$2

if [ ! -f $fname ]; then
echo "$fname not available locally, downloading.."
wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
fi
}

pushd test-data
get_data $LOOM_LINK $BASENAME_FILE"_loom.h5"
get_data $RDS_LINK $BASENAME_FILE".rds"
get_data $SCE_LINK $BASENAME_FILE"_sce.rds"
get_data $H5AD_LINK $BASENAME_FILE".h5ad"
23 changes: 19 additions & 4 deletions tools/tertiary-analysis/sceasy/sceasy_convert.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="utf-8"?>
<tool id="sceasy_convert" name="SCEasy convert" version="@TOOL_VERSION@+galaxy1">
<tool id="sceasy_convert" name="SCEasy convert" version="@TOOL_VERSION@+galaxy0">
<description>a data object between formats</description>
<macros>
<import>sceasy_macros.xml</import>
Expand Down Expand Up @@ -84,16 +84,31 @@
<data name="output_loom" format="h5" from_work_dir="output.loom" label="${tool.name} on ${on_string}: Loom">
<filter>conversion['direction'].endswith('loom')</filter>
</data>
<data name="output_anndata" format="h5" from_work_dir="output.h5ad" label="${tool.name} on ${on_string}: AnnData">
<data name="output_anndata" format="h5ad" from_work_dir="output.h5ad" label="${tool.name} on ${on_string}: AnnData">
<filter>conversion['direction'].endswith('anndata')</filter>
</data>
</outputs>

<tests>
<test>
<param name="direction" value="loom2sce"/>
<param name="input_object_file" value="input.loom"/>
<output name="output_sce" file="output.rds" ftype="rdata" compare="sim_size"/>
<param name="input_object_file" value="E-MTAB-6077-3k_features_90_cells_loom.h5"/>
<output name="output_sce" file="E-MTAB-6077-3k_features_90_cells_sce.rds" ftype="rdata" compare="sim_size"/>
</test>
<test>
<param name="direction" value="sce2loom"/>
<param name="input_object_file" value="E-MTAB-6077-3k_features_90_cells_sce.rds"/>
<output name="output_sce" file="E-MTAB-6077-3k_features_90_cells_loom.h5" ftype="h5" compare="sim_size"/>
</test>
<test>
<param name="direction" value="sce2anndata"/>
<param name="input_object_file" value="E-MTAB-6077-3k_features_90_cells_sce.rds"/>
<output name="output_sce" file="E-MTAB-6077-3k_features_90_cells.h5ad" ftype="h5" compare="sim_size"/>
</test>
<test>
<param name="direction" value="seurat2anndata"/>
<param name="input_object_file" value="E-MTAB-6077-3k_features_90_cells.rds"/>
<output name="output_sce" file="E-MTAB-6077-3k_features_90_cells.h5ad" ftype="h5ad" compare="sim_size"/>
</test>
</tests>

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5 changes: 3 additions & 2 deletions tools/tertiary-analysis/sceasy/sceasy_macros.xml
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@@ -1,15 +1,16 @@
<macros>
<token name="@TOOL_VERSION@">0.0.5</token>
<token name="@TOOL_VERSION@">0.0.7</token>
<token name="@HELP@">More information can be found at https://github.com/cellgeni/sceasy</token>
<token name="@VERSION_HISTORY@"><![CDATA[
**Version history**
0.0.7+galaxy0: Moves to SCEasy 0.0.7

0.0.1+galaxy0: Initial version based on sceasy 0.0.5 by Ni Huang, WTSI.
]]></token>

<xml name="requirements">
<requirements>
<requirement type="package" version="0.0.5">r-sceasy</requirement>
<requirement type="package" version="0.0.7">r-sceasy</requirement>
<yield/>
</requirements>
</xml>
Expand Down